biotite 1.4.0__cp313-cp313-macosx_11_0_arm64.whl → 1.5.0__cp313-cp313-macosx_11_0_arm64.whl

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Files changed (46) hide show
  1. biotite/application/dssp/app.py +63 -6
  2. biotite/database/afdb/download.py +12 -6
  3. biotite/database/rcsb/download.py +1 -0
  4. biotite/database/rcsb/query.py +2 -2
  5. biotite/sequence/align/banded.cpython-313-darwin.so +0 -0
  6. biotite/sequence/align/kmeralphabet.cpython-313-darwin.so +0 -0
  7. biotite/sequence/align/kmersimilarity.cpython-313-darwin.so +0 -0
  8. biotite/sequence/align/kmertable.cpython-313-darwin.so +0 -0
  9. biotite/sequence/align/localgapped.cpython-313-darwin.so +0 -0
  10. biotite/sequence/align/localungapped.cpython-313-darwin.so +0 -0
  11. biotite/sequence/align/multiple.cpython-313-darwin.so +0 -0
  12. biotite/sequence/align/pairwise.cpython-313-darwin.so +0 -0
  13. biotite/sequence/align/permutation.cpython-313-darwin.so +0 -0
  14. biotite/sequence/align/selector.cpython-313-darwin.so +0 -0
  15. biotite/sequence/align/tracetable.cpython-313-darwin.so +0 -0
  16. biotite/sequence/codec.cpython-313-darwin.so +0 -0
  17. biotite/sequence/phylo/nj.cpython-313-darwin.so +0 -0
  18. biotite/sequence/phylo/tree.cpython-313-darwin.so +0 -0
  19. biotite/sequence/phylo/upgma.cpython-313-darwin.so +0 -0
  20. biotite/structure/atoms.py +1 -1
  21. biotite/structure/bonds.cpython-313-darwin.so +0 -0
  22. biotite/structure/celllist.cpython-313-darwin.so +0 -0
  23. biotite/structure/chains.py +34 -0
  24. biotite/structure/charges.cpython-313-darwin.so +0 -0
  25. biotite/structure/filter.py +2 -1
  26. biotite/structure/geometry.py +164 -2
  27. biotite/structure/info/atoms.py +8 -0
  28. biotite/structure/info/components.bcif +0 -0
  29. biotite/structure/io/pdb/convert.py +1 -0
  30. biotite/structure/io/pdb/file.py +16 -2
  31. biotite/structure/io/pdb/hybrid36.cpython-313-darwin.so +0 -0
  32. biotite/structure/io/pdbx/bcif.py +1 -1
  33. biotite/structure/io/pdbx/cif.py +1 -1
  34. biotite/structure/io/pdbx/compress.py +13 -9
  35. biotite/structure/io/pdbx/convert.py +17 -6
  36. biotite/structure/io/pdbx/encoding.cpython-313-darwin.so +0 -0
  37. biotite/structure/io/pdbx/encoding.pyx +39 -8
  38. biotite/structure/residues.py +173 -1
  39. biotite/structure/sasa.cpython-313-darwin.so +0 -0
  40. biotite/structure/segments.py +39 -3
  41. biotite/structure/util.py +14 -22
  42. biotite/version.py +16 -3
  43. {biotite-1.4.0.dist-info → biotite-1.5.0.dist-info}/METADATA +1 -1
  44. {biotite-1.4.0.dist-info → biotite-1.5.0.dist-info}/RECORD +46 -46
  45. {biotite-1.4.0.dist-info → biotite-1.5.0.dist-info}/WHEEL +0 -0
  46. {biotite-1.4.0.dist-info → biotite-1.5.0.dist-info}/licenses/LICENSE.rst +0 -0
@@ -1,8 +1,8 @@
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- biotite-1.4.0.dist-info/RECORD,,
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- biotite-1.4.0.dist-info/WHEEL,sha256=s0cTlxH34_QlWnER2EjFUsHTyO2KntcvTrX9yBtBmNo,133
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- biotite-1.4.0.dist-info/METADATA,sha256=NZDvKedU4WJkuZIOpWAI3GXJIdbfP5jDh_CbaLSLfgU,5525
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- biotite-1.4.0.dist-info/licenses/LICENSE.rst,sha256=ZuNQuB65Dxf0rDB_5LxvA4SVQJBWxRZyvbjbvE-APWY,1534
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- biotite/version.py,sha256=rcWNYDlh913lujUvTfOu9iOIPdrTXg64R9wl7ENLjFU,511
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+ biotite-1.5.0.dist-info/RECORD,,
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+ biotite-1.5.0.dist-info/WHEEL,sha256=s0cTlxH34_QlWnER2EjFUsHTyO2KntcvTrX9yBtBmNo,133
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+ biotite-1.5.0.dist-info/METADATA,sha256=UUKw6ATrAZtUc-I5_CvIIate_rM_OP8QyhHmLKF2tjY,5525
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+ biotite-1.5.0.dist-info/licenses/LICENSE.rst,sha256=ZuNQuB65Dxf0rDB_5LxvA4SVQJBWxRZyvbjbvE-APWY,1534
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+ biotite/version.py,sha256=sfeo6QRBwy3wEFaKhAEbFPpF98FLjoe4Car1c6NnghQ,704
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  biotite/copyable.py,sha256=C7ycTQxqanxT0SmXhzy5OLp7NpZdNWHyokozdoVDGNA,1897
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  biotite/__init__.py,sha256=rL8ZyaCUjOrECEvRxyHj8MOMp4FHMJ8n6KKgrYf5OAQ,545
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  biotite/visualize.py,sha256=GSxIL8PLXMDlaULG-ckSghRifQnBnkseZ-OWsnuno4M,13955
@@ -25,10 +25,10 @@ biotite/database/pubchem/query.py,sha256=Z_DVRY62HhelCtMr3xwUOZBBUpNCwTKVC8ey9dG
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  biotite/database/pubchem/download.py,sha256=p1UtPJ1YuccDWLsXE4Zd410RwqgbwCHj5ZDcISQ6-5U,9870
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  biotite/database/pubchem/__init__.py,sha256=xjwfutIL4-JeTs7v4wCkRyy5q4KE7fGWDvo46ubkXt4,669
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  biotite/database/pubchem/throttle.py,sha256=HXf2l7EW5RLdW0bg72uSdXCDZXFXOE49akhfgKhEdc8,3286
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- biotite/database/rcsb/query.py,sha256=Ar2uZRuOCMm0RQeMATHfAeTeW5G8eNfg2Iy5qMMZ8JU,32895
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- biotite/database/rcsb/download.py,sha256=AtRljEV60NReeuWno-YFNrzrpFY_hetghO31-8VojtE,5676
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+ biotite/database/rcsb/query.py,sha256=svweSjUNDOuZRLDfYTN17goFPOeHKhHs_qPvi9VkKs8,32897
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+ biotite/database/rcsb/download.py,sha256=a2Epoari3qItLTbBpjKWgBL-H4tbOAP9UQlUnhkXSS4,5757
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  biotite/database/rcsb/__init__.py,sha256=sTJnL4vYwhO7gSszMuT_Lr91uwX0wM1h-fZWiZkITYA,332
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- biotite/database/afdb/download.py,sha256=sIaGz0hTj1MBA_XIw9HCP6NGnPfNAyPgryOhLuRa9i8,6367
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+ biotite/database/afdb/download.py,sha256=cSi6x4KXSDHBm4qv7-dK4Q4k09uefNSoVGZjHWHfjQs,6679
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  biotite/database/afdb/__init__.py,sha256=VqRn4WE6wJWS4Sd916xchmMz7tyPpEflnwOVnInhEOs,333
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  biotite/interface/version.py,sha256=1duxoIDwBB6onugS5QqrM1iyM_O644Dw0FGai0V9ssc,2952
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  biotite/interface/__init__.py,sha256=CEbr_8h6pt3za2ybSeePcNKMsA2vkNUbzYhzP62g2Lg,717
@@ -52,7 +52,7 @@ biotite/application/__init__.py,sha256=gOy5iGp5uuKTd0qpR9LgsmanB3ZfdQaTnZcKMRDwS
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  biotite/application/application.py,sha256=MLMft5z1ocBMsTOXkUg-ZeZj0jC8l6WHrYSjgkE7iW8,8096
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  biotite/application/msaapp.py,sha256=6e88Q7vgGSK_5uKdOVPcZF6wMKDRGYEKrvc9tb0yjbs,11974
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  biotite/application/dssp/__init__.py,sha256=lUf-A2rJzPLJYZQZGpZUt7HtA0M59KaX6zQSCrkhfF4,323
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- biotite/application/dssp/app.py,sha256=tHoG8uFmX8WaBHm0Fhjc7D0NXEaMa-zkLvwFzyP4FQk,5323
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+ biotite/application/dssp/app.py,sha256=Xs0A764NKchkGFVEfB4bqBinFC5r2wNyAmKEk4G06dQ,7612
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  biotite/application/viennarna/rnaalifold.py,sha256=QawXG9hYKQzdRt8-J_WiXUcoJx7Whps-iSCzq7DFJEA,10683
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  biotite/application/viennarna/util.py,sha256=racSlWGMtRRNtc_wh-ggIJWPDNoxIqwejc_Ztgusk8Q,2635
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  biotite/application/viennarna/__init__.py,sha256=m2obwXBnkDzRDzjrffsGdnp7YxAFz6CctsSmmg03xVI,473
@@ -80,7 +80,7 @@ biotite/sequence/sequence.py,sha256=eIZ7Ugz9IwXlWXs_HC2NGyAtDDcP-Vf1z82jynT_PPE,
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  biotite/sequence/profile.py,sha256=f-KYMVtSB83O5J0Jy87Nzetd4axZDVsUcMSES2J7MJY,19249
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  biotite/sequence/codon_tables.txt,sha256=zZLT642H4qEkwUk5g-hWh-6ZWP_bgaz70fWcxwJDWJ0,10209
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  biotite/sequence/__init__.py,sha256=fSWhobaPGRMJI6-8UYFpjguxVtP4O4cAHmiRxNAGzYI,3423
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- biotite/sequence/codec.cpython-313-darwin.so,sha256=rDMx0TdL9kK2_Ly3thWUGTdI8xnOp22NBsAHs7WDuNo,286456
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+ biotite/sequence/codec.cpython-313-darwin.so,sha256=hArEwOnCle2O6DIzF1UXDrEkEqz_3hwJoBNHxz6gQL8,332040
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  biotite/sequence/seqtypes.py,sha256=I5OaC9IOJoA9G610Tod67cgCWDQqTAgYpK1FHF8Ofok,23246
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  biotite/sequence/codon.py,sha256=Scua9XHD-TnWfCaKHRegKQGSP3XK3wW3zLgxen45ux0,16346
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  biotite/sequence/search.py,sha256=G__T-GHMJODWmgh87z5wxs_g9-t1DtvEOd-USp-Qizg,3088
@@ -101,36 +101,36 @@ biotite/sequence/io/genbank/file.py,sha256=5XvuJCd_FuI2zh03_bLbLSAuORNw4tXr7p9sG
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  biotite/sequence/io/fastq/convert.py,sha256=x4rWn7WHdKxW1u7mwDgM8Z3qaML4lAO7r-JiMTQbvaI,3632
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  biotite/sequence/io/fastq/__init__.py,sha256=lhw9bxWS0eKPXzF1lg8fvrNmgAmJPLBzIB6jEP5GOVI,588
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  biotite/sequence/io/fastq/file.py,sha256=Q5jrBN21Fi0hp6rU5cc68kQPYc1jWdZfMwhx0Ze6oGw,17817
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- biotite/sequence/align/multiple.cpython-313-darwin.so,sha256=hBq9Fi0unR_5Zs_SQkAxfGyZrXymHNyc51bAN78wQqs,463264
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- biotite/sequence/align/permutation.cpython-313-darwin.so,sha256=W7P5BUEJDsYeBBwZKO4zZH36JATOxrlVORutEFSm8Gs,232080
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+ biotite/sequence/align/multiple.cpython-313-darwin.so,sha256=XGhGbF-0ylJVooe1VB54hsxYfMsqomHMvSerOa_UXpU,547824
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+ biotite/sequence/align/permutation.cpython-313-darwin.so,sha256=W5T0l61UZIT3cXj6B8gHmkhSM3tM9W2HXgydtyTyBL0,256528
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  biotite/sequence/align/selector.pyx,sha256=BstkOkz-nB2dPtkZIZbU5QlCT-h3QHxdsGg1pGUh-Qo,33471
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- biotite/sequence/align/pairwise.cpython-313-darwin.so,sha256=warnRCepn0o6W4EcuSfJDFz8G93wZV2Zi4QdfYBUktg,553168
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+ biotite/sequence/align/pairwise.cpython-313-darwin.so,sha256=sfEoLw5-pjWlyptkUCa8ZFGxUBD46Pn8V8EozMNPjY8,679536
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- biotite/sequence/align/localgapped.cpython-313-darwin.so,sha256=qdxTHjYK0fA6wGe9_ziK2q29gquDQOC3Dv8SnZwN8T4,1016320
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- biotite/sequence/align/banded.cpython-313-darwin.so,sha256=9hwd0KSAeWCM2OF3qaUqP-n-Ea6TUFPton7x5uUM5Dg,514832
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+ biotite/sequence/align/localgapped.cpython-313-darwin.so,sha256=5rzV9EQkhFOQy29gbFzxa12t8qfubEmR292I7n-Hc5I,1184592
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+ biotite/sequence/align/banded.cpython-313-darwin.so,sha256=Zui26C3ar45yPh_j52WFo0SuwMifwBViU6PqwMsNrDs,619840
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- biotite/sequence/align/localungapped.cpython-313-darwin.so,sha256=uRLro5PnImSM7bRKpE_HXYWTtP6FyCk_2pHiXQBOulA,305536
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+ biotite/sequence/align/localungapped.cpython-313-darwin.so,sha256=DxyXYXtdaaWP3aV61v2VxC4Jq9jEUX5HNw5x-1r-bbo,354032
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- biotite/sequence/align/selector.cpython-313-darwin.so,sha256=xzKfUdho6sAoMGyzThQNkHNzpTe1f7awiNEZr4oKQBw,307952
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+ biotite/sequence/align/selector.cpython-313-darwin.so,sha256=rUaesp6aj1a0qNx8f3Hc5wsRRniIPQ7-cpBbLyuh23M,343168
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- biotite/sequence/align/kmeralphabet.cpython-313-darwin.so,sha256=NwMD7V8n-TSeA4UGOxqLd_3r2IfkIqecCOImWBCGAq8,388128
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+ biotite/sequence/align/kmeralphabet.cpython-313-darwin.so,sha256=hmIW6XXV97anKc9DgyAp1JG6ABmfH4zHKb127DLDr_k,457664
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- biotite/sequence/align/kmertable.cpython-313-darwin.so,sha256=qRTkRAHIOhON80-ofe4ydFCs20M_Beia9MegS7o300Y,655232
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+ biotite/sequence/align/kmertable.cpython-313-darwin.so,sha256=F3qc3EZIpC38LGtm0ZonazwyITJW_dl0MWBPxqCcE0g,755744
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- biotite/sequence/align/kmersimilarity.cpython-313-darwin.so,sha256=u4wl8V8A4j-N__1J3CnE0czYR5KClwmxbkJhHxhrv2I,213544
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+ biotite/sequence/align/kmersimilarity.cpython-313-darwin.so,sha256=lv9Xlf8zgYHRcvc5V2C6S0F5Hahq9t_en37wM1qoBC0,255160
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- biotite/sequence/align/tracetable.cpython-313-darwin.so,sha256=mRQIdttZYZNOYB3S5-0bCeglu0UWg1Nik_vRd4xwg3Q,186256
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+ biotite/sequence/align/tracetable.cpython-313-darwin.so,sha256=wpOJMHNjvmAp3mpL-r8TwtyC-hWPL8_C76nwNf9hlSk,207344
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@@ -251,47 +251,47 @@ biotite/sequence/graphics/color_schemes/jalview_zappo.json,sha256=V0IJ-GsT8G8-J9
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- biotite/sequence/phylo/tree.cpython-313-darwin.so,sha256=BtJYZtbcQMxMyeGMJVQqqdInM8KC4BWALWU1rme0X2U,267336
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- biotite/sequence/phylo/upgma.cpython-313-darwin.so,sha256=yHPFJvYPal8E4o7ZveJpmOYkS-tV3wwMjl3nA_L8cOk,210648
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+ biotite/sequence/phylo/tree.cpython-313-darwin.so,sha256=ymJi2OpReUoFYsXGBMagJEupCa8aXntgrmNVuVWibJ4,314072
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+ biotite/sequence/phylo/upgma.cpython-313-darwin.so,sha256=lA7EsOa9UjFdKSHOrjLbXiZXLFWeWgz-1mUuAPhzj-4,232872
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+ biotite/sequence/phylo/nj.cpython-313-darwin.so,sha256=oAiP4BDFg3mjRtUrrgH6ryO43IzvLRZBkHjnLFOpWmY,233768
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- biotite/structure/bonds.cpython-313-darwin.so,sha256=0s2JxPkZOlNN60AvCpYxwpTdzGtqe8wb_jiTULbWECM,549080
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+ biotite/structure/chains.py,sha256=pp0GUo3Nc75lUy19mgv6E6F-QyWZJKo44AyY3H5fNpY,9347
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+ biotite/structure/celllist.cpython-313-darwin.so,sha256=YOCWQUELackBzA_Kv6fA5QmGI6qIDDONqVhJdFKisLA,338048
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@@ -302,13 +302,13 @@ biotite/structure/io/dcd/__init__.py,sha256=tYiiTSmqDrsSgg_sZaoQgx2D8N9OeqlooxH4
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- biotite/structure/io/pdbx/bcif.py,sha256=y5ueesX3G-5JSVj0chX6LiJ71IYdjgaF5x0nR6stiD0,21247
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- biotite/structure/io/pdbx/convert.py,sha256=hEBw0QeRNGRX70z3W0i7cDjVgIOD7RFrOnZGrUMa_gM,79916
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+ biotite/structure/io/pdbx/bcif.py,sha256=8dQyPCtQho4tV2dRK52hOsifOOGnXPMLI7SDJt_UgaU,21248
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+ biotite/structure/io/pdbx/convert.py,sha256=gNdslGuHHQwixoacevhxLgUpCtY3AZEvSNUYvP0W3UQ,80733
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+ biotite/structure/io/pdbx/encoding.cpython-313-darwin.so,sha256=NcGmLMY64zDvO3s8viOfahL1JPHdrco4yEXOFamlT1I,1332096
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+ biotite/structure/io/pdbx/encoding.pyx,sha256=gqTnq2qONPRdv5lz2JkJIhjK4k3J9k-Fp8YOVbeE9N0,33609
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- biotite/structure/io/pdbx/cif.py,sha256=1gyMDANR51yNXsV0aFIAK4VSUYl32nBIC94RwQf57PE,34978
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+ biotite/structure/io/pdbx/compress.py,sha256=YAUaMsaXwmxpFOnbYgkrTl4k-k3PiBXyC6tKWAajxfI,13407
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+ biotite/structure/io/pdbx/cif.py,sha256=1hY4-brq_kX_Hg5-OJm600zcdXV6KDidZhTdHKQunYY,34979
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@@ -325,10 +325,10 @@ biotite/structure/io/mol/__init__.py,sha256=WvcNPDdf9W1zPyJ0tjTvGNxA83ht18uRQA8B
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- biotite/structure/io/pdb/convert.py,sha256=ECG8KFmduPN2xd7HWqJweYabn-IFdnhxVNtO3AkzLaQ,13800
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- biotite/structure/io/pdb/hybrid36.cpython-313-darwin.so,sha256=wXBho7x3UDSuZKX8-OQRB9fte-gFy4VKFm2Ie1f63Nk,193936
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+ biotite/structure/io/pdb/convert.py,sha256=nnRZl5cG5N6UQURG_oSfLZ1z32uXeiF9pOMcpOTFNcI,13826
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+ biotite/structure/io/pdb/hybrid36.cpython-313-darwin.so,sha256=-AyGs8pjtsLMoqRBIPYWP6G8Eiw9h_cwyua5hU56Ajc,235904
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- biotite/structure/io/pdb/file.py,sha256=Ppb0bFqmp8xi-L-_dA3JzEuMBjLdUUJKZEDB4DUeblw,54085
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+ biotite/structure/io/pdb/file.py,sha256=GCS8qD-efyXswe5acr2Erz3qurGfY52J60n06BqA7jc,54557
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@@ -338,7 +338,7 @@ biotite/structure/alphabet/encoder.py,sha256=2BWLMdGBr2bHw09vMhbzPztMKSnVt8UhUf8
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+ biotite/structure/info/components.bcif,sha256=mQrO6PEOkPNw2i1DHp5qugNyDx0g-2d_uV-T4KD1bwI,62070945
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@@ -347,7 +347,7 @@ biotite/structure/info/radii.py,sha256=PGpl5WoaFBzAktxNodzb_mCz8jp0AwW3GNXk9jKN3
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+ biotite/structure/info/atoms.py,sha256=8GoHM5owz0-Tnx9OzV8Q41sz-WU7TAJfy4sTgAW939Q,3271
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